6-100477898-T-C

Position:

• chr6-100477898-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.487 in 152,016 control chromosomes in the GnomAD database, including 18,263 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (18263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74011 AN: 151898 Hom.: 18251 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.499

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.487 AC: 74043 AN: 152016 Hom.: 18263 Cov.: 32 AF XY: 0.488 AC XY: 36232 AN XY: 74316

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.494

Alfa AF: 0.505 Hom.: 7048

Bravo AF: 0.471

Asia WGS AF: 0.473 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6910391; hg19: chr6-100925774; COSMIC: COSV69415975;